Ebola virus was first identified as a possible new "strain" of Marburg virus in 1976. At the same time, a third team introduced the name "Ebola virus", derived from the Ebola River where the 1976 outbreak occurred. The International Committee on Taxonomy of Viruses (ICTV) identifies Ebola virus as species Zaire ebolavirus, which is included into the genus Ebolavirus, family Filoviridae, order Mononegavirales. The name "Ebola virus" is derived from the Ebola River—a river that was at first thought to be in close proximity to the area in Democratic Republic of Congo, previously called Zaire, where the 1976 Zaire Ebola virus outbreak occurred—and the taxonomic suffix virus.

In 2000, the virus name was changed to Zaire Ebola virus, and in 2002 to species Zaire ebolavirus. However, most scientific articles continued to refer to "Ebola virus" or used the terms Ebola virus and Zaire ebolavirus in parallel. Consequently, in 2010, a group of researchers recommended that the name "Ebola virus" be adopted for a subclassification within the species Zaire ebolavirus, with the corresponding abbreviation EBOV. Previous abbreviations for the virus were EBOV-Z (for Ebola virus Zaire) and ZEBOV (for Zaire Ebola virus or Zaire ebolavirus). In 2011, the ICTV explicitly rejected a proposal (2010.010bV) to recognize this name, as ICTV does not designate names for subtypes, variants, strains, or other subspecies level groupings. At present, ICTV does not officially recognize "Ebola virus" as a taxonomic rank, and rather continues to use and recommend only the species designation Zaire ebolavirus.